Professor of biology Graham Walker watches two Holliston High School students -- Hannah Cohen, left, and Kristen Mirageas -- explore the PDBViewer in the TEAL classroom in the basement of the Stata Center on Friday, March 31.

Protein viewer unveiled

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Last week, 200 high school biology students on a field trip to campus became the first to use a new 3-D protein database viewer that was created at MIT and will soon be available to schools nationwide.

The viewer was created by researchers in three different MIT departments, including Professor Graham Walker of biology, who used part of a $1 million Howard Hughes Medical Institute grant to form the HHMI Education Group, a research group dedicated to training science educators and developing tools and curriculum to improve introductory biology courses.

"Proteins are three-dimensional entities and we need to understand them that way," Walker said. But the professional viewers available were "powerful but complicated to use," he said. The ones made for educational purposes were "much more limited in their capabilities," but still difficult to use, he said.

In recent months, members of the HHMI Education Group collaborated to create the new protein database viewer using an educational tool developed several years ago at the MIT Center for Educational Computing Initiatives for the MIT physics department. That tool, the Technology Enhanced Active Learning Simulation Environment (TEALsim), was designed by Andrew McKinney, Phillip Bailey and Michael Danziger. It uses computer graphics to simulate physics problems, making them easier for students to visualize and understand, said Professor John Belcher of physics.

If TEALsim worked for physics, the team thought it might also work for biology.

Using the TEALsim architecture, Walker and his research team joined forces with Danziger and Ivica Ceraj of Information Systems and Technology (IS&T) to create the PDBViewer, which has much of the power of the professional viewers, but is both easy to use and visually appealing. They plan to introduce it into several MIT courses next year.

The PDBViewer was unveiled to the MIT community in the TEAL classroom in the basement of the Stata Center on Wednesday, March 29. On March 30 and 31, students from eight area high schools came for a science field trip, which Walker's group has run annually since 2003 during the MIT spring break. High school students tour labs, attend lectures and participate in lab work led by graduate students.

Last year, the students attended a lab using an older protein viewer, the SwissPDBViewer. Their teachers remembered the problems they had with that program and this year they praised the new PDBViewer. "This is such a gorgeous program," said Mary Aguirre, a biology teacher at Hudson High, who was jumping up and down with excitement over the new viewer. "It gives you such an amazing visual of what is going on."

Working in pairs, the high school students spent an hour on a tutorial program, first looking at the structure of the protein hemoglobin. By clicking the mouse, they could rotate the hemoglobin molecule, move it up and down and zoom in on specific areas. They were able to quickly answer questions about the shape and structure of hemoglobin.

Although they worked steadily, few studnts raised their hands with questions -- a huge change from last year, said Melissa Kosinski-Collins, a postdoctoral associate in Walker's lab. "Last year there had to be two graduate students per table," she said.

"This is great," said Kimberly Greco, a sophomore at Holliston High School. "The graphics are incredible and we picked up on it in a matter of minutes."

Collaboration was the key to this project, said the viewer's creators. "It has been an absolute joy," said Charles Shubert, a software architect from IS&T. "It has so far surpassed our expectations."